BRATTLEBORO — Vermont Yankee nuclear power plant will be allowed to continue discharging millions of gallons of heated water into the Connecticut River until the plant shuts down later this year, despite owner Entergy Nuclear relying on “flawed science,” a draft state permit released Thursday stated.

But under new conditions included in the permit, Entergy might have to curb its discharge this fall, so that the temperature of the Connecticut River climbs no higher than 69 degrees. The current limit is 71, said Deb Markowitz, secretary of the Agency of Natural Resources.

The Connecticut River water is heated as part of the process to keep the reactor cool during fission; the river water never comes in direct contact with radioactive materials.

Environmental groups had fought Entergy for years about the permit because of the effect of the higher temperatures on fish, particularly the migrating American shad during the spring, and the river’s biota.

The permit expired almost nine years ago but had been grandfathered by the state as several Clean Water Act challenges were settled in federal court, as well as challenges to new Environmental Protection Agency rules.

The permit makes clear that if Vermont Yankee weren’t shutting down at the end of the year, its thermal discharge into the Connecticut River would have to change.

Opponents to the permit had claimed the heated water was killing fish, particularly American shad, as Entergy was asking for increasing levels of hot water discharge to save money and not using its cooling towers as much.

Markowitz said the draft permit would trigger a public comment period. A public hearing will be held in mid-August in Vernon, the agency said.

Markowitz said the state’s experts disagreed with the scientific methodology Entergy used to assess the effect of the large warm water discharge.

“I’m very proud of the work of our staff,” said Markowitz. “It’s a meaningful permit, and it’s reasonable in its expectations.”

“Our technical experts disagreed with the standard that Vermont Yankee has relied on. I would say we had a difference of opinion,” she said.

Entergy issued a measured response Thursday afternoon. “We are reviewing the draft permit. ... While it is too early to speculate on our position on any of the issues, I can tell you that Vermont Yankee’s operation is compliant with the existing (National Pollutant Discharge Elimination System) permit and fully protective of the Connecticut River. We look forward to participating in the public comment process,” wrote Rob Williams, Entergy Nuclear spokesman, via email.

The Connecticut River Watershed Council said it understood the decision on the permit.

“We are right on the science but reluctantly understand the necessity to allow Entergy to operate using that flawed Equation 1.1 through their closure in December 2014 because there is an additional requirement that the river not get hotter than the permit allows,” said the watershed council’s executive director, Andy Fisk.

While the Shumlin administration had reached a far-ranging agreement with Entergy in December covering many aspects of the reactor’s remaining operation and closure, the discharge permit wasn’t one of them.

Raymond Shadis, senior technical adviser for the New England Coalition, which had fought the thermal discharge permit, said the watershed council’s efforts were reflected in the new permit.

“However, in the big picture, ANR’s tougher thermal limits will likely mean more to some future would-be polluter than they will to Entergy VY,” Shadis said.

“The permit is not likely to take effect for two or more months, and thus its effective river protections can only be enforced for three or four months trending into cold weather, when thermal discharge is less of an issue.”